Genetic and epigenetic fine mapping of causal autoimmune disease variants

Supplemental table 1 has genomic coordinates of disease-associated SNPs.

Analysis of TFBSs

Out of all regulatory datasets, we select only TFBSs.

## [1] 1954   39
## [1] 1259   38

Text mining question 1: Are the diseases within a cluster share stronger literature similarity than the diseases between the clusters? To answer, we need literature similarity scores for each pair, then split the pairs into cluster-specific groups and compare score distributions with what can be expected by chance, calculating the p-values for it. Expected answer: Diseases within each cluster are related to each other by literature findings stronger than could be expected by chance. Diseases between the clusters are not related to each other by literature findings, and this also may be statistically significant.

The top 10 pairs of disease-associated SNPs are most similar with each other.

## 
## -----------------------------------------------------------------------------------------------
##                   Disease 1                             Disease 2            Corr. coefficient 
## ---------------------------------------------- ---------------------------- -------------------
##                HDL_cholesterol                        Triglycerides               0.5484       
## 
##                Kawasaki_disease                Systemic_lupus_erythematosus       0.5352       
## 
##              Bone_mineral_density                    Type_2_diabetes              0.5268       
## 
##                Kawasaki_disease                     Multiple_sclerosis             0.501       
## 
##                Kawasaki_disease                    Rheumatoid_arthritis           0.4775       
## 
##                 Celiac_disease                       Kawasaki_disease             0.4754       
## 
##                LDL_cholesterol                        Triglycerides               0.4743       
## 
##                Kawasaki_disease                     Ulcerative_colitis            0.4661       
## 
## Liver_enzyme_levels_gamma_glutamyl_transferase         Urate_levels               0.4191       
## 
##              Alzheimers_combined                   Bone_mineral_density           0.4149       
## -----------------------------------------------------------------------------------------------

The similarity dendrogram can be divided into separate groups:

## Cluster01 has   8 members 
## Kawasaki_disease
## Systemic_lupus_erythematosus
## Celiac_disease
## Ulcerative_colitis
## Psoriasis
## Multiple_sclerosis
## Rheumatoid_arthritis
## Allergy
##  
## Cluster02 has  12 members 
## Systemic_sclerosis
## Primary_biliary_cirrhosis
## Atopic_dermatitis
## Juvenile_idiopathic_arthritis
## Ankylosing_spondylitis
## Crohns_disease
## Type_1_diabetes
## Primary_sclerosing_cholangitis
## Creatinine_levels
## Behcets_disease
## Progressive_supranuclear_palsy
## Restless_legs_syndrome
##  
## Cluster03 has   8 members 
## Vitiligo
## Migraine
## Alopecia_areata
## Asthma
## Chronic_kidney_disease
## Alzheimers_combined
## Bone_mineral_density
## Type_2_diabetes
##  
## Cluster04 has  10 members 
## Urate_levels
## Liver_enzyme_levels_gamma_glutamyl_transferase
## LDL_cholesterol
## HDL_cholesterol
## Triglycerides
## Renal_function_related_traits_BUN
## Platelet_counts
## Red_blood_cell_traits
## C_reactive_protein
## Fasting_glucose_related_traits
## 

The “Enrichment 1/2” columns show the average p-values of the group-specific SNPs-regulatory associations. A “-” sign indicates that an association is underrepresented. The “p-value” column shows whether the difference in the associations between the groups is statistically significantly different.

## [1] "c1 vs. c2 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 86"
## 
## -------------------------------------------------------------------------------------------------------------
##                     Row.names                                   V2                  c1       c2    adj.P.Val 
## -------------------------------------------------- ----------------------------- --------- ------ -----------
##      wgEncodeSydhTfbsGm18505NfkbTnfaIggrabPk         GM18505 NFKB IgG-rab TNFa   3.594e-06 0.9272   0.03671  
##                                                         ChIP-seq Peaks from                                  
##                                                             ENCODE/SYDH                                      
## 
##        wgEncodeSydhTfbsGm12878Pol2IggmusPk         GM12878 Pol2 IgG-mus ChIP-seq 9.774e-06 0.8334  0.003843  
##                                                       Peaks from ENCODE/SYDH                                 
## 
##  wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep2     GM12878 MTA3 v042211.1     2.011e-05 0.7491  0.0002624 
##                                                      ChIP-seq Peaks Rep 2 from                               
##                                                             ENCODE/HAIB                                      
## 
##        wgEncodeSydhTfbsGm12891Pol2IggmusPk         GM12891 Pol2 IgG-mus ChIP-seq 6.286e-05 0.6297   0.03649  
##                                                       Peaks from ENCODE/SYDH                                 
## 
##  wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1     GM12878 NFIC v042211.1     6.767e-05 0.5832  0.000109  
##                                                      ChIP-seq Peaks Rep 1 from                               
##                                                             ENCODE/HAIB                                      
## 
## wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep2   GM12878 NFATC1 v042211.1    9.584e-05 0.6672  0.0006969 
##                                                      ChIP-seq Peaks Rep 2 from                               
##                                                             ENCODE/HAIB                                      
## 
##     wgEncodeHaibTfbsGm12892Pol2V0416102PkRep1         GM12892 Pol2 v041610.2     0.0001446 0.7113  0.004147  
##                                                      ChIP-seq Peaks Rep 1 from                               
##                                                             ENCODE/HAIB                                      
## 
##    wgEncodeSydhTfbsGm12878Chd1a301218aIggmusPk     GM12878 CHD1 IgG-mus ChIP-seq 0.0001594 0.7835  0.004317  
##                                                       Peaks from ENCODE/SYDH                                 
## 
##     wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep1         GM12878 Pol2-4H8 PCR1x     0.0002028 0.965    0.05724  
##                                                      ChIP-seq Peaks Rep 1 from                               
##                                                             ENCODE/HAIB                                      
## 
##  wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep2       GM12878 PML v042211.1     0.0001479 0.7001   8.3e-05  
##                                                      ChIP-seq Peaks Rep 2 from                               
##                                                             ENCODE/HAIB                                      
## -------------------------------------------------------------------------------------------------------------
## 
## [1] "c1 vs. c3 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 110"
## 
## ---------------------------------------------------------------------------------------------------------------
##                     Row.names                                   V2                  c1        c3     adj.P.Val 
## -------------------------------------------------- ----------------------------- --------- -------- -----------
##  wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep2     GM12878 MTA3 v042211.1     2.011e-05 -0.03223  9.655e-06 
##                                                      ChIP-seq Peaks Rep 2 from                                 
##                                                             ENCODE/HAIB                                        
## 
##        wgEncodeSydhTfbsGm12878Pol2IggmusPk         GM12878 Pol2 IgG-mus ChIP-seq 9.774e-06 -0.06673  0.0006752 
##                                                       Peaks from ENCODE/SYDH                                   
## 
##      wgEncodeSydhTfbsGm18505NfkbTnfaIggrabPk         GM18505 NFKB IgG-rab TNFa   3.594e-06 -0.4501    0.03447  
##                                                         ChIP-seq Peaks from                                    
##                                                             ENCODE/SYDH                                        
## 
##        wgEncodeSydhTfbsGm12891Pol2IggmusPk         GM12891 Pol2 IgG-mus ChIP-seq 6.286e-05 -0.1467    0.01099  
##                                                       Peaks from ENCODE/SYDH                                   
## 
##  wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1     GM12878 NFIC v042211.1     6.767e-05 -0.1369   8.824e-06 
##                                                      ChIP-seq Peaks Rep 1 from                                 
##                                                             ENCODE/HAIB                                        
## 
##     wgEncodeHaibTfbsGm12892Pol2V0416102PkRep1         GM12892 Pol2 v041610.2     0.0001446 -0.09939  0.0005075 
##                                                      ChIP-seq Peaks Rep 1 from                                 
##                                                             ENCODE/HAIB                                        
## 
## wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep2   GM12878 NFATC1 v042211.1    9.584e-05 -0.1597   8.211e-05 
##                                                      ChIP-seq Peaks Rep 2 from                                 
##                                                             ENCODE/HAIB                                        
## 
##  wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep2       GM12878 PML v042211.1     0.0001479 -0.1222   8.824e-06 
##                                                      ChIP-seq Peaks Rep 2 from                                 
##                                                             ENCODE/HAIB                                        
## 
##        wgEncodeSydhTfbsGm18505Pol2IggmusPk         GM18505 Pol2 IgG-mus ChIP-seq 0.0002114 -0.1043   0.0003008 
##                                                       Peaks from ENCODE/SYDH                                   
## 
##    wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep1     GM12892 Pol2-4H8 v041610.2   0.0003613 -0.06464  0.000142  
##                                                      ChIP-seq Peaks Rep 1 from                                 
##                                                             ENCODE/HAIB                                        
## ---------------------------------------------------------------------------------------------------------------
## 
## [1] "c1 vs. c4 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 103"
## 
## --------------------------------------------------------------------------------------------------------------
##                     Row.names                                   V2                  c1       c4     adj.P.Val 
## -------------------------------------------------- ----------------------------- --------- ------- -----------
##      wgEncodeSydhTfbsGm18505NfkbTnfaIggrabPk         GM18505 NFKB IgG-rab TNFa   3.594e-06 -0.775    0.03454  
##                                                         ChIP-seq Peaks from                                   
##                                                             ENCODE/SYDH                                       
## 
##        wgEncodeSydhTfbsGm12878Pol2IggmusPk         GM12878 Pol2 IgG-mus ChIP-seq 9.774e-06 -0.3918  0.001616  
##                                                       Peaks from ENCODE/SYDH                                  
## 
##  wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep2     GM12878 MTA3 v042211.1     2.011e-05 -0.2356  3.528e-05 
##                                                      ChIP-seq Peaks Rep 2 from                                
##                                                             ENCODE/HAIB                                       
## 
##  wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1     GM12878 NFIC v042211.1     6.767e-05 -0.1347  5.071e-06 
##                                                      ChIP-seq Peaks Rep 1 from                                
##                                                             ENCODE/HAIB                                       
## 
##        wgEncodeSydhTfbsGm12891Pol2IggmusPk         GM12891 Pol2 IgG-mus ChIP-seq 6.286e-05 -0.5071   0.01766  
##                                                       Peaks from ENCODE/SYDH                                  
## 
##  wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep2       GM12878 PML v042211.1     0.0001479 -0.3198  9.171e-06 
##                                                      ChIP-seq Peaks Rep 2 from                                
##                                                             ENCODE/HAIB                                       
## 
## wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep2   GM12878 NFATC1 v042211.1    9.584e-05 -0.4966  0.0001887 
##                                                      ChIP-seq Peaks Rep 2 from                                
##                                                             ENCODE/HAIB                                       
## 
##  wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep1     GM12878 MTA3 v042211.1     0.000339   -0.2    2.35e-05  
##                                                      ChIP-seq Peaks Rep 1 from                                
##                                                             ENCODE/HAIB                                       
## 
##     wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep2         GM12878 Pol2-4H8 PCR1x     0.0004474 -0.1903  0.004696  
##                                                      ChIP-seq Peaks Rep 2 from                                
##                                                             ENCODE/HAIB                                       
## 
##     wgEncodeHaibTfbsGm12892Pol2V0416102PkRep1         GM12892 Pol2 v041610.2     0.0001446 -0.6038   0.00179  
##                                                      ChIP-seq Peaks Rep 1 from                                
##                                                             ENCODE/HAIB                                       
## --------------------------------------------------------------------------------------------------------------
## 
## [1] "c2 vs. c3 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 0"
## 
## -------------------------------------------------------------------------------------------------------------
##                    Row.names                                  V2                  c2        c3     adj.P.Val 
## ------------------------------------------------ ----------------------------- --------- -------- -----------
##  wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep2       MCF-7 HDAC2 v042211.1     1.024e-08 -0.9111    0.6711   
##                                                    ChIP-seq Peaks Rep 2 from                                 
##                                                           ENCODE/HAIB                                        
## 
## wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep1  A549 TEAD4 v042211.1 ChIP-seq 2.584e-07  0.7003    0.6885   
##                                                  Peaks Rep 1 from ENCODE/HAIB                                
## 
##       wgEncodeSydhTfbsMcf7Gata3sc269UcdPk         MCF-7 GATA3 SC269 UC Davis   5.462e-06 -0.9907    0.6676   
##                                                       ChIP-seq Peaks from                                    
##                                                           ENCODE/SYDH                                        
## 
##         wgEncodeSydhTfbsH1hescSuz12UcdPk            H1-hESC SUZ12 UC Davis     5.736e-06  0.3309    0.7192   
##                                                       ChIP-seq Peaks from                                    
##                                                           ENCODE/SYDH                                        
## 
##      wgEncodeHaibTfbsMcf7MaxV0422111PkRep2       MCF-7 Max v042211.1 ChIP-seq  0.0001833  0.8041    0.6885   
##                                                  Peaks Rep 2 from ENCODE/HAIB                                
## 
##     wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep1          MCF-7 TCF12 v042211.1     0.002079   0.9427    0.6192   
##                                                    ChIP-seq Peaks Rep 1 from                                 
##                                                           ENCODE/HAIB                                        
## 
##       wgEncodeSydhTfbsGm12878JundIggrabPk        GM12878 JunD IgG-rab ChIP-seq  0.02161  -0.9099    0.7584   
##                                                     Peaks from ENCODE/SYDH                                   
## 
## wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep2    GM12878 MTA3 v042211.1      0.7491   -0.03223   0.4004   
##                                                    ChIP-seq Peaks Rep 2 from                                 
##                                                           ENCODE/HAIB                                        
## 
##    wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep2       HL-60 Pol2-4H8 v042211.1     0.0397    -0.657    0.4988   
##                                                    ChIP-seq Peaks Rep 2 from                                 
##                                                           ENCODE/HAIB                                        
## 
##   wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep1    GM12892 Pol2-4H8 v041610.2    0.4503   -0.06464   0.3761   
##                                                    ChIP-seq Peaks Rep 1 from                                 
##                                                           ENCODE/HAIB                                        
## -------------------------------------------------------------------------------------------------------------
## 
## [1] "c2 vs. c4 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 0"
## 
## ------------------------------------------------------------------------------------------------------------
##                    Row.names                                  V2                  c2       c4     adj.P.Val 
## ------------------------------------------------ ----------------------------- --------- ------- -----------
##  wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep2       MCF-7 HDAC2 v042211.1     1.024e-08 0.7626    0.8601   
##                                                    ChIP-seq Peaks Rep 2 from                                
##                                                           ENCODE/HAIB                                       
## 
## wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep1  A549 TEAD4 v042211.1 ChIP-seq 2.584e-07 0.8079    0.8601   
##                                                  Peaks Rep 1 from ENCODE/HAIB                               
## 
##       wgEncodeSydhTfbsMcf7Gata3sc269UcdPk         MCF-7 GATA3 SC269 UC Davis   5.462e-06 0.9893    0.8463   
##                                                       ChIP-seq Peaks from                                   
##                                                           ENCODE/SYDH                                       
## 
##         wgEncodeSydhTfbsH1hescSuz12UcdPk            H1-hESC SUZ12 UC Davis     5.736e-06 0.8414    0.8601   
##                                                       ChIP-seq Peaks from                                   
##                                                           ENCODE/SYDH                                       
## 
##      wgEncodeHaibTfbsMcf7MaxV0422111PkRep2       MCF-7 Max v042211.1 ChIP-seq  0.0001833 0.8538    0.8601   
##                                                  Peaks Rep 2 from ENCODE/HAIB                               
## 
##     wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep1          MCF-7 TCF12 v042211.1     0.002079  0.8988    0.8204   
##                                                    ChIP-seq Peaks Rep 1 from                                
##                                                           ENCODE/HAIB                                       
## 
##       wgEncodeSydhTfbsGm12878JundIggrabPk        GM12878 JunD IgG-rab ChIP-seq  0.02161  -0.9997   0.9213   
##                                                     Peaks from ENCODE/SYDH                                  
## 
##    wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep2       HL-60 Pol2-4H8 v042211.1     0.0397   -0.7606   0.7664   
##                                                    ChIP-seq Peaks Rep 2 from                                
##                                                           ENCODE/HAIB                                       
## 
##    wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep2        GM12878 Pol2-4H8 PCR1x      0.3719   -0.1903   0.8628   
##                                                    ChIP-seq Peaks Rep 2 from                                
##                                                           ENCODE/HAIB                                       
## 
## wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1    GM12878 NFIC v042211.1      0.5832   -0.1347   0.6952   
##                                                    ChIP-seq Peaks Rep 1 from                                
##                                                           ENCODE/HAIB                                       
## ------------------------------------------------------------------------------------------------------------
## 
## [1] "c3 vs. c4 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 0"
## 
## -----------------------------------------------------------------------------------------------------------
##                     Row.names                                   V2                 c3     c4     adj.P.Val 
## -------------------------------------------------- ----------------------------- ------ ------- -----------
##          wgEncodeSydhTfbsK562Pol2s2StdPk               K562 Pol2 S2 Standard     0.143  -0.8604   0.2013   
##                                                         ChIP-seq Peaks from                                
##                                                             ENCODE/SYDH                                    
## 
##      wgEncodeSydhTfbsImr90Mazab85725IggrabPk        IMR90 MAZ (ab85725) IgG-rab  0.1393 0.6184    0.6938   
##                                                         ChIP-seq Peaks from                                
##                                                             ENCODE/SYDH                                    
## 
## wgEncodeAwgTfbsSydhH1hescSin3anb6001263IggrabUniPk H1-hESC TFBS Uniform Peaks of 0.2549 0.9992     0.221   
##                                                       SIN3A_(NB600-1263) from                              
##                                                      ENCODE/Stanford/Analysis                              
## 
##        wgEncodeUwTfbsBjCtcfStdHotspotsRep1             BJ CTCF TFBS ChIP-seq     0.2954 -0.8671   0.1851   
##                                                      Hotspots 1 from ENCODE/UW                             
## 
##        wgEncodeUwTfbsHmfCtcfStdHotspotsRep1           HMF CTCF TFBS ChIP-seq     0.2174 0.8316    0.1651   
##                                                      Hotspots 1 from ENCODE/UW                             
## 
##     wgEncodeHaibTfbsHct116Rad21V0422111PkRep1         HCT-116 RAD21 v042211.1    0.334  -0.9289   0.1625   
##                                                      ChIP-seq Peaks Rep 1 from                             
##                                                             ENCODE/HAIB                                    
## 
##      wgEncodeHaibTfbsEcc1Rad21V0422111PkRep2           ECC-1 RAD21 v042211.1     0.3424 -0.9585   0.1651   
##                                                      ChIP-seq Peaks Rep 2 from                             
##                                                             ENCODE/HAIB                                    
## 
##       wgEncodeUwTfbsHbmecCtcfStdHotspotsRep1         HBMEC CTCF TFBS ChIP-seq     0.32  0.9727    0.1651   
##                                                      Hotspots 1 from ENCODE/UW                             
## 
##  wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02PkRep1     A549 CTCF 5916 EtOH PCR1x   0.3365 -0.9842   0.1625   
##                                                      ChIP-seq Peaks Rep 1 from                             
##                                                             ENCODE/HAIB                                    
## 
##       wgEncodeAwgTfbsSydhH1hescSuz12UcdUniPk       H1-hESC TFBS Uniform Peaks of 0.3232 0.9742    0.4938   
##                                                             SUZ12 from                                     
##                                                         ENCODE/USC/Analysis                                
## -----------------------------------------------------------------------------------------------------------

Text mining question 2: Are the terms associated stronger with the diseases in one vs. the other cluster based on the literature strength? Are the terms themselves related based on the literature? Expected answer: Yes, the literature associations should confirm the relationships.

Summary

  1. There are 4 clusters. The first cluster drives all the differences.
C1 C2 C3 C4
C1 Cell types: Gm12878 Reg: NFkB, Pol2, MTA3, NFIC, NFATC1 Cell types: Gm12878 Reg: NFkB, Pol2, MTA3, NFIC, NFATC1 Cell types: Gm12878 Reg: NFkB, Pol2, MTA3, NFIC, NFATC1
C2 Nothing significant Nothing significant
C3 Nothing significant
C4

Analysis of histone marks

Out of all regulatory datasets, we select only histone marks

## [1] 721  39
## [1] 610  39

Text mining question 1: Are the diseases within a cluster share stronger literature similarity than the diseases between the clusters? To answer, we need literature similarity scores for each pair, then split the pairs into cluster-specific groups and compare score distributions with what can be expected by chance, calculating the p-values for it. Expected answer: Diseases within each cluster are related to each other by literature findings stronger than could be expected by chance. Diseases between the clusters are not related to each other by literature findings, and this also may be statistically significant.

The top 10 pairs of autoimmune-associated SNPs are most similar with each other.

## 
## ---------------------------------------------------------------------------------------
##             Disease 1                         Disease 2              Corr. coefficient 
## --------------------------------- --------------------------------- -------------------
##          HDL_cholesterol                    Triglycerides                  0.621       
## 
##       Rheumatoid_arthritis               Ulcerative_colitis               0.4856       
## 
##          HDL_cholesterol                   LDL_cholesterol                 0.48        
## 
##          HDL_cholesterol                   Platelet_counts                0.4609       
## 
##          Platelet_counts                    Triglycerides                 0.4504       
## 
##          LDL_cholesterol                    Triglycerides                 0.4151       
## 
##         Creatinine_levels         Renal_function_related_traits_BUN       0.3915       
## 
##             Psoriasis               Systemic_lupus_erythematosus          0.3911       
## 
## Renal_function_related_traits_BUN           Urate_levels                  0.3689       
## 
##          Alopecia_areata                 C_reactive_protein               0.3686       
## ---------------------------------------------------------------------------------------

The similarity dendrogram can be divided into separate groups:

## Cluster01 has   6 members 
## Celiac_disease
## Multiple_sclerosis
## Kawasaki_disease
## Primary_biliary_cirrhosis
## Systemic_lupus_erythematosus
## Psoriasis
##  
## Cluster02 has  14 members 
## Type_2_diabetes
## Fasting_glucose_related_traits
## Red_blood_cell_traits
## Crohns_disease
## Migraine
## Systemic_sclerosis
## Ankylosing_spondylitis
## Platelet_counts
## Triglycerides
## HDL_cholesterol
## Vitiligo
## Progressive_supranuclear_palsy
## Liver_enzyme_levels_gamma_glutamyl_transferase
## LDL_cholesterol
##  
## Cluster03 has  11 members 
## Allergy
## Type_1_diabetes
## Primary_sclerosing_cholangitis
## Juvenile_idiopathic_arthritis
## Behcets_disease
## Ulcerative_colitis
## Rheumatoid_arthritis
## Autoimmune_thyroiditis
## Alopecia_areata
## C_reactive_protein
## Asthma
##  
## Cluster04 has   8 members 
## Bone_mineral_density
## Chronic_kidney_disease
## Alzheimers_combined
## Restless_legs_syndrome
## Atopic_dermatitis
## Urate_levels
## Renal_function_related_traits_BUN
## Creatinine_levels
## 

The “Enrichment 1/2” columns show the average p-values of the group-specific SNPs-regulatory associations. A “-” sign indicates that an association is underrepresented. The “p-value” column shows whether the difference in the associations bwtween the groups is statistically significantly different.

## [1] "c1 vs. c2 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 45"
## 
## ---------------------------------------------------------------------------------------------------------
##                 Row.names                               V2                  c1         c2      adj.P.Val 
## ------------------------------------------ ----------------------------- --------- ---------- -----------
## wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 GM12878 H3K4me1 Histone Mods  6.263e-15  -0.01015   3.557e-05 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneGm12878H3k9me3StdPk   GM12878 H3K9me3 Histone Mods  2.129e-10 -0.0002502  3.665e-05 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##   wgEncodeBroadHistoneGm12878H3k9acStdPk    GM12878 H3K9ac Histone Mods  3.849e-12   -0.205    8.601e-07 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneGm12878H3k27acStdPk   GM12878 H3K27ac Histone Mods  2.561e-11  -0.1967    0.0003686 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##    wgEncodeBroadHistoneGm12878H2azStdPk    GM12878 H2A.Z Histone Mods by 8.379e-11  -0.0708    0.002582  
##                                                 ChIP-seq Peaks from                                      
##                                                    ENCODE/Broad                                          
## 
##     wgEncodeBroadHistoneCd20H3k04me2Pk     CD20+ H3K4me2 Histone Mods by  6.1e-09   -0.06418   3.557e-05 
##                                                 ChIP-seq Peaks from                                      
##                                                    ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneGm12878H3k4me2StdPk   GM12878 H3K4me2 Histone Mods  8.782e-09  -0.06392   8.601e-07 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneCd20ro01794H3k27acPk  CD20+ RO01794 H3K27ac Histone 1.057e-08  -0.09878   0.005575  
##                                             Mods by ChIP-seq Peaks from                                  
##                                                    ENCODE/Broad                                          
## 
##       wgEncodeBroadHistoneCd20H2azPk        CD20+ H2A.Z Histone Mods by  5.608e-08  -0.03372   0.000703  
##                                                 ChIP-seq Peaks from                                      
##                                                    ENCODE/Broad                                          
## 
## wgEncodeBroadHistoneGm12878H3k04me3StdPkV2 GM12878 H3K4me3 Histone Mods  4.708e-08   -0.167    2.222e-05 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## ---------------------------------------------------------------------------------------------------------
## 
## [1] "c1 vs. c3 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 47"
## 
## ------------------------------------------------------------------------------------------------------
##                 Row.names                               V2                  c1       c3     adj.P.Val 
## ------------------------------------------ ----------------------------- --------- ------- -----------
## wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 GM12878 H3K4me1 Histone Mods  6.263e-15 0.2686   0.001041  
##                                               by ChIP-seq Peaks from                                  
##                                                    ENCODE/Broad                                       
## 
##   wgEncodeBroadHistoneGm12878H3k9acStdPk    GM12878 H3K9ac Histone Mods  3.849e-12 0.2791   2.209e-05 
##                                               by ChIP-seq Peaks from                                  
##                                                    ENCODE/Broad                                       
## 
##  wgEncodeBroadHistoneGm12878H3k27acStdPk   GM12878 H3K27ac Histone Mods  2.561e-11 0.1264   0.004196  
##                                               by ChIP-seq Peaks from                                  
##                                                    ENCODE/Broad                                       
## 
##    wgEncodeBroadHistoneGm12878H2azStdPk    GM12878 H2A.Z Histone Mods by 8.379e-11 0.2377    0.01882  
##                                                 ChIP-seq Peaks from                                   
##                                                    ENCODE/Broad                                       
## 
##  wgEncodeBroadHistoneCd20ro01794H3k27acPk  CD20+ RO01794 H3K27ac Histone 1.057e-08 -0.4077   0.01648  
##                                             Mods by ChIP-seq Peaks from                               
##                                                    ENCODE/Broad                                       
## 
##  wgEncodeBroadHistoneGm12878H3k9me3StdPk   GM12878 H3K9me3 Histone Mods  2.129e-10 0.03993   0.01648  
##                                               by ChIP-seq Peaks from                                  
##                                                    ENCODE/Broad                                       
## 
##     wgEncodeBroadHistoneCd20H3k04me2Pk     CD20+ H3K4me2 Histone Mods by  6.1e-09  0.7209   0.000875  
##                                                 ChIP-seq Peaks from                                   
##                                                    ENCODE/Broad                                       
## 
##  wgEncodeBroadHistoneGm12878H3k79me2StdPk  GM12878 H3K79me2 Histone Mods 1.867e-08 -0.4995  7.28e-05  
##                                               by ChIP-seq Peaks from                                  
##                                                    ENCODE/Broad                                       
## 
##  wgEncodeBroadHistoneGm12878H3k4me2StdPk   GM12878 H3K4me2 Histone Mods  8.782e-09 0.5631   5.197e-05 
##                                               by ChIP-seq Peaks from                                  
##                                                    ENCODE/Broad                                       
## 
##    wgEncodeBroadHistoneDnd41H3k04me1Pk     Dnd41 H3K4me1 Histone Mods by 9.105e-08 -0.7878  0.0001171 
##                                                 ChIP-seq Peaks from                                   
##                                                    ENCODE/Broad                                       
## ------------------------------------------------------------------------------------------------------
## 
## [1] "c1 vs. c4 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 58"
## 
## ---------------------------------------------------------------------------------------------------------
##                 Row.names                               V2                  c1         c4      adj.P.Val 
## ------------------------------------------ ----------------------------- --------- ---------- -----------
## wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 GM12878 H3K4me1 Histone Mods  6.263e-15 -0.008689   0.0001299 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneGm12878H3k9me3StdPk   GM12878 H3K9me3 Histone Mods  2.129e-10 -1.413e-05  5.165e-05 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneGm12878H3k27acStdPk   GM12878 H3K27ac Histone Mods  2.561e-11 -0.007023   0.0002497 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##   wgEncodeBroadHistoneGm12878H3k9acStdPk    GM12878 H3K9ac Histone Mods  3.849e-12  -0.1383    4.143e-06 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneCd20ro01794H3k27acPk  CD20+ RO01794 H3K27ac Histone 1.057e-08 -0.001005   0.001851  
##                                             Mods by ChIP-seq Peaks from                                  
##                                                    ENCODE/Broad                                          
## 
##    wgEncodeBroadHistoneGm12878H2azStdPk    GM12878 H2A.Z Histone Mods by 8.379e-11   -0.161    0.008068  
##                                                 ChIP-seq Peaks from                                      
##                                                    ENCODE/Broad                                          
## 
##     wgEncodeBroadHistoneCd20H3k04me2Pk     CD20+ H3K4me2 Histone Mods by  6.1e-09   -0.01543   6.552e-05 
##                                                 ChIP-seq Peaks from                                      
##                                                    ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneGm12878H3k79me2StdPk  GM12878 H3K79me2 Histone Mods 1.867e-08 -0.005656   5.047e-06 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneGm12878H3k4me2StdPk   GM12878 H3K4me2 Histone Mods  8.782e-09  -0.02811   4.143e-06 
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## 
## wgEncodeBroadHistoneGm12878H3k04me3StdPkV2 GM12878 H3K4me3 Histone Mods  4.708e-08  -0.01621   2.43e-05  
##                                               by ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                          
## ---------------------------------------------------------------------------------------------------------
## 
## [1] "c2 vs. c3 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 32"
## 
## --------------------------------------------------------------------------------------------------------
##                 Row.names                               V2                  c2        c3      adj.P.Val 
## ------------------------------------------ ----------------------------- --------- --------- -----------
##   wgEncodeBroadHistoneK562H3k36me3StdPk    K562 H3K36me3 Histone Mods by 0.001587  -0.009793   0.03505  
##                                                 ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                         
## 
##   wgEncodeBroadHistoneNhekH4k20me1StdPk    NHEK H4K20me1 Histone Mods by 0.0009324  -0.0364    0.06562  
##                                                 ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                         
## 
##    wgEncodeBroadHistoneNhdfadH4k20me1Pk    NHDF-Ad H4K20me1 Histone Mods 0.001681  -0.02737    0.04472  
##                                               by ChIP-seq Peaks from                                    
##                                                    ENCODE/Broad                                         
## 
##     wgEncodeBroadHistoneNhaH3k79me2Pk      NH-A H3K79me2 Histone Mods by  0.01045  -0.01294    0.01579  
##                                                 ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                         
## 
## wgEncodeBroadHistoneA549H3k79me2Dex100nmPk   A549 DEX 100 nM H3K79me2    0.008678  -0.02115    0.01579  
##                                              Histone Mods by ChIP-seq                                   
##                                               Peaks from ENCODE/Broad                                   
## 
##     wgEncodeBroadHistoneNhlfH3k79me2Pk     NHLF H3K79me2 Histone Mods by 0.005332  -0.05179    0.03198  
##                                                 ChIP-seq Peaks from                                     
##                                                    ENCODE/Broad                                         
## 
##    wgEncodeBroadHistoneNhdfadH3k79me2Pk    NHDF-Ad H3K79me2 Histone Mods  0.01755  -0.02178    0.03732  
##                                               by ChIP-seq Peaks from                                    
##                                                    ENCODE/Broad                                         
## 
##  wgEncodeBroadHistoneA549H3k36me3Etoh02Pk    A549 EtOH 0.02% H3K36me3     0.01319  -0.03129    0.02689  
##                                              Histone Mods by ChIP-seq                                   
##                                               Peaks from ENCODE/Broad                                   
## 
##    wgEncodeBroadHistoneOsteoH3k79me2Pk     Osteoblasts H3K79me2 Histone   0.02111  -0.01993    0.01579  
##                                             Mods by ChIP-seq Peaks from                                 
##                                                    ENCODE/Broad                                         
## 
##  wgEncodeBroadHistoneA549H3k79me2Etoh02Pk    A549 EtOH 0.02% H3K79me2     0.01245  -0.03612    0.02647  
##                                              Histone Mods by ChIP-seq                                   
##                                               Peaks from ENCODE/Broad                                   
## --------------------------------------------------------------------------------------------------------
## 
## [1] "c2 vs. c4 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 9"
## 
## -------------------------------------------------------------------------------------------------------
##                Row.names                              V2                  c2         c4      adj.P.Val 
## ---------------------------------------- ----------------------------- --------- ---------- -----------
##  wgEncodeBroadHistoneHmecH3k36me3StdPk   HMEC H3K36me3 Histone Mods by  0.01773  -0.0002847   0.04273  
##                                               ChIP-seq Peaks from                                      
##                                                  ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneK562H3k36me3StdPk   K562 H3K36me3 Histone Mods by 0.001587   -0.00739    0.1287   
##                                               ChIP-seq Peaks from                                      
##                                                  ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneNhekH4k20me1StdPk   NHEK H4K20me1 Histone Mods by 0.0009324  -0.05835     0.198   
##                                               ChIP-seq Peaks from                                      
##                                                  ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneK562Nsd2ab75359Pk    K562 NSD2 (ab75359) Histone  0.001909   -0.03803    0.1947   
##                                           Mods by ChIP-seq Peaks from                                  
##                                                  ENCODE/Broad                                          
## 
##      wgEncodeBroadHistoneK562RestPk        K562 REST Histone Mods by   0.007983   -0.01042    0.1487   
##                                               ChIP-seq Peaks from                                      
##                                                  ENCODE/Broad                                          
## 
##   wgEncodeBroadHistoneNhdfadH4k20me1Pk   NHDF-Ad H4K20me1 Histone Mods 0.001681   -0.1255     0.2067   
##                                             by ChIP-seq Peaks from                                     
##                                                  ENCODE/Broad                                          
## 
##      wgEncodeBroadHistoneK562NcorPk        K562 NCoR Histone Mods by    0.04478  -0.005174    0.0846   
##                                               ChIP-seq Peaks from                                      
##                                                  ENCODE/Broad                                          
## 
## wgEncodeBroadHistoneGm12878H3k36me3StdPk GM12878 H3K36me3 Histone Mods  0.2219   -0.001063    0.05838  
##                                             by ChIP-seq Peaks from                                     
##                                                  ENCODE/Broad                                          
## 
##   wgEncodeBroadHistoneNhekH3k9me1StdPk   NHEK H3K9me1 Histone Mods by   0.2002   -0.001186    0.02253  
##                                               ChIP-seq Peaks from                                      
##                                                  ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneHepg2H3k36me3StdPk   HepG2 H3K36me3 Histone Mods   0.03916  -0.006255    0.1623   
##                                             by ChIP-seq Peaks from                                     
##                                                  ENCODE/Broad                                          
## -------------------------------------------------------------------------------------------------------
## 
## [1] "c3 vs. c4 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 0"
## 
## ------------------------------------------------------------------------------------------------------
##                Row.names                             V2                  c3         c4      adj.P.Val 
## --------------------------------------- ----------------------------- --------- ---------- -----------
##  wgEncodeBroadHistoneHsmmH3k27me3StdPk  HSMM H3K27me3 Histone Mods by 3.654e-07  -0.02171    0.4638   
##                                              ChIP-seq Peaks from                                      
##                                                 ENCODE/Broad                                          
## 
## wgEncodeBroadHistoneGm12878H3k9me3StdPk GM12878 H3K9me3 Histone Mods   0.03993  -1.413e-05   0.6051   
##                                            by ChIP-seq Peaks from                                     
##                                                 ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneHmecH3k27me3StdPk  HMEC H3K27me3 Histone Mods by 5.588e-06  -0.1737     0.6051   
##                                              ChIP-seq Peaks from                                      
##                                                 ENCODE/Broad                                          
## 
## wgEncodeBroadHistoneNhdfadH3k27me3StdPk NHDF-Ad H3K27me3 Histone Mods 0.0002821  -0.08736    0.6051   
##                                            by ChIP-seq Peaks from                                     
##                                                 ENCODE/Broad                                          
## 
##   wgEncodeBroadHistoneHmecEzh239875Pk     HMEC EZH2 (39875) Histone   0.006694  -0.008291    0.6051   
##                                          Mods by ChIP-seq Peaks from                                  
##                                                 ENCODE/Broad                                          
## 
##   wgEncodeBroadHistoneOsteoH3k27me3Pk   Osteoblasts H3K27me3 Histone  0.0006062  -0.1426     0.6051   
##                                          Mods by ChIP-seq Peaks from                                  
##                                                 ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneNhaH3k27me3StdPk   NH-A H3K27me3 Histone Mods by 0.0001926  -0.9361     0.6051   
##                                              ChIP-seq Peaks from                                      
##                                                 ENCODE/Broad                                          
## 
##  wgEncodeBroadHistoneOsteoP300kat3bPk      Osteoblasts P300 KAT3B     0.0004775  -0.5556     0.6051   
##                                           Histone Mods by ChIP-seq                                    
##                                            Peaks from ENCODE/Broad                                    
## 
## wgEncodeBroadHistoneGm12878Ezh239875Pk  GM12878 EZH2 (39875) Histone   0.02094   -0.01915    0.6051   
##                                          Mods by ChIP-seq Peaks from                                  
##                                                 ENCODE/Broad                                          
## 
## wgEncodeBroadHistoneHepg2H3k27me3StdPk   HepG2 H3K27me3 Histone Mods  0.0008383  -0.6783     0.6051   
##                                            by ChIP-seq Peaks from                                     
##                                                 ENCODE/Broad                                          
## ------------------------------------------------------------------------------------------------------

Text mining question 2: Are the terms associated stronger with the diseases in one vs. the other cluster based on the literature strength? Are the terms themselves related based on the literature? Expected answer: Yes, the literature associations should confirm the relationships.

Summary

  1. Again, cluster 1 is strongly distinct. Cluster 2 is less so. Histone marks seem all active.
C1 C2 C3 C4
C1 Cell types: Gm12878, CD20+ Reg: H3K4me1, H3K9me3, H3K9ac, H3K27ac, H2az, H3K4me2 Cell types: Gm12878, CD20+ Reg: H3K4me1, H3K9me3, H3K9ac, H3K27ac, H2az, H3K4me2 Cell types: Gm12878, CD20+ Reg: H3K4me1, H3K9me3, H3K9ac, H3K27ac, H2az, H3K4me2
C2 Cell types: K562, NHEK, NHDF-Ad, NH-A, HMEC Reg: H3K36me3, H4K20me1, H3K79me2 Nothing significant
C3 Nothing significant
C4

Analysis of all regulatory datasets

Out of all regulatory datasets, we select all. The goal here is to get potentially tighter clustering.

## [1] 4498   39
## [1] 2969   39

The top 10 pairs of disease-associated SNPs are most similar with each other.

## 
## --------------------------------------------------------------------------------------------
##                   Disease 1                            Disease 2          Corr. coefficient 
## ---------------------------------------------- ------------------------- -------------------
##                HDL_cholesterol                       Triglycerides              0.473       
## 
##                LDL_cholesterol                       Triglycerides             0.4314       
## 
##             Chronic_kidney_disease                   Urate_levels              0.3742       
## 
##                HDL_cholesterol                      LDL_cholesterol            0.3475       
## 
##              Bone_mineral_density                   Type_2_diabetes            0.3225       
## 
##               Multiple_sclerosis               Primary_biliary_cirrhosis        0.316       
## 
##              Alzheimers_combined                    Type_2_diabetes            0.2999       
## 
## Liver_enzyme_levels_gamma_glutamyl_transferase       Urate_levels              0.2976       
## 
##         Fasting_glucose_related_traits              Type_2_diabetes            0.2972       
## 
## Liver_enzyme_levels_gamma_glutamyl_transferase      Platelet_counts            0.2944       
## --------------------------------------------------------------------------------------------

The similarity dendrogram can be divided into separate groups:

## Cluster01 has  14 members 
## Platelet_counts
## Liver_enzyme_levels_gamma_glutamyl_transferase
## Red_blood_cell_traits
## LDL_cholesterol
## HDL_cholesterol
## Triglycerides
## Type_2_diabetes
## Fasting_glucose_related_traits
## Bone_mineral_density
## Alzheimers_combined
## Creatinine_levels
## Renal_function_related_traits_BUN
## Urate_levels
## Chronic_kidney_disease
##  
## Cluster02 has  25 members 
## Multiple_sclerosis
## Kawasaki_disease
## Celiac_disease
## Systemic_lupus_erythematosus
## Psoriasis
## Ulcerative_colitis
## Rheumatoid_arthritis
## Crohns_disease
## Autoimmune_thyroiditis
## Primary_biliary_cirrhosis
## Ankylosing_spondylitis
## Systemic_sclerosis
## Migraine
## Primary_sclerosing_cholangitis
## Juvenile_idiopathic_arthritis
## Atopic_dermatitis
## Alopecia_areata
## C_reactive_protein
## Allergy
## Type_1_diabetes
## Vitiligo
## Behcets_disease
## Progressive_supranuclear_palsy
## Restless_legs_syndrome
## Asthma
## 

The “Enrichment 1/2” columns show the average p-values of the group-specific SNPs-regulatory associations. A “-” sign indicates that an association is underrepresented. The “p-value” column shows whether the difference in the associations bwtween the groups is statistically significantly different.

## [1] "c1 vs. c2 , number of degs significant at adj.p.val<0.5 and 2-fold diff: 0"
## 
## --------------------------------------------------------------------------------------------------------------
##                     Row.names                                  V2                  c1        c2     adj.P.Val 
## ------------------------------------------------- ----------------------------- --------- -------- -----------
##   wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep2       MCF-7 HDAC2 v042211.1     1.561e-07  0.8353    0.4918   
##                                                     ChIP-seq Peaks Rep 2 from                                 
##                                                            ENCODE/HAIB                                        
## 
##  wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep1  A549 TEAD4 v042211.1 ChIP-seq 2.373e-06  0.7976    0.4968   
##                                                   Peaks Rep 1 from ENCODE/HAIB                                
## 
##         wgEncodeSydhTfbsH1hescSuz12UcdPk             H1-hESC SUZ12 UC Davis     1.619e-05  0.6341    0.4822   
##                                                        ChIP-seq Peaks from                                    
##                                                            ENCODE/SYDH                                        
## 
##        wgEncodeSydhTfbsMcf7Gata3sc269UcdPk         MCF-7 GATA3 SC269 UC Davis   4.078e-05  0.7946    0.5005   
##                                                        ChIP-seq Peaks from                                    
##                                                            ENCODE/SYDH                                        
## 
##    wgEncodeGisChiaPetMcf7EraaInteractionsRep2       MCF-7 ERalpha a ChIA-PET    0.0008577 -0.1465    0.1052   
##                                                      Interactions Rep 2 from                                  
##                                                          ENCODE/GIS-Ruan                                      
## 
##       wgEncodeBroadHistoneNhekH4k20me1StdPk       NHEK H4K20me1 Histone Mods by 0.003353  -0.0967    0.1683   
##                                                        ChIP-seq Peaks from                                    
##                                                           ENCODE/Broad                                        
## 
## wgEncodeCshlLongRnaSeqK562ChromatinTotalJunctions K562 chromatin total RNA-seq   0.02711  -0.01382   0.3846   
##                                                       Junctions Pooled from                                   
##                                                            ENCODE/CSHL                                        
## 
##    wgEncodeGisRnaPetK562NucleusPapClustersRep1         K562 nucleus polyA+      0.005089  -0.07474   0.1233   
##                                                   clone-based RNA PET Clusters                                
##                                                       Rep 1 from ENCODE/GIS                                   
## 
##  wgEncodeGisRnaPetK562ChromatinTotalClustersRep1      K562 chromatin total       0.01422  -0.03698   0.1849   
##                                                   clone-based RNA PET Clusters                                
##                                                       Rep 1 from ENCODE/GIS                                   
## 
##   wgEncodeGisRnaPetHepg2CytosolPapClustersRep1        HepG2 cytosol polyA+      0.006008  -0.1193    0.1068   
##                                                   clone-based RNA PET Clusters                                
##                                                       Rep 1 from ENCODE/GIS                                   
## --------------------------------------------------------------------------------------------------------------

Summary

The picture is not as good as when we are taking subsets of regulatory datasets.